Variant report

Variant	rs12620113
Chromosome Location	chr2:85936833-85936834
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85934009..85937395-chr2:85940314..85944557,5	MCF-7	breast:
2	chr2:85846395..85848017-chr2:85935471..85937032,2	K562	blood:
3	chr2:85932175..85937503-chr2:85937871..85941981,7	K562	blood:
4	chr2:85936798..85938889-chr2:85946240..85947988,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10180391	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10180445	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10180451	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10180547	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187164	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187314	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10187495	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192752	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10203826	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10210321	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714150	0.83[ASN][1000 genomes]
rs12845	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13389847	0.97[ASN][1000 genomes]
rs13408224	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1437742	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1437743	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1437744	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1437745	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561284	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561285	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1837115	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866138	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1866139	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1866140	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs1866141	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2043760	0.82[JPT][hapmap]
rs2070966	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118402	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366805	0.82[ASN][1000 genomes]
rs2366807	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2886767	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2886768	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34218330	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34702373	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34771575	0.90[ASN][1000 genomes]
rs34943381	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35616630	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3755007	0.90[ASN][1000 genomes]
rs4240200	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240201	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4240202	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4832181	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4832183	0.86[JPT][hapmap]
rs4832185	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4832187	0.85[ASN][1000 genomes]
rs55665393	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59832218	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61191323	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62163092	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740635	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585576	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880872	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874465	chr2:85898898-85939207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv874466	chr2:85909026-85939207	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874467	chr2:85916487-85946708	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12620113	AC012454.4	cis	Whole Blood	GTEx
rs12620113	ATOH8	cis	Whole Blood	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85926000-85945200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:85931200-85941600	Enhancers	Liver	Liver
3	chr2:85931400-85937800	Enhancers	Adipose Nuclei	Adipose
4	chr2:85931600-85941000	Enhancers	Primary hematopoietic stem cells	blood
5	chr2:85932400-85941400	Enhancers	Brain Hippocampus Middle	brain
6	chr2:85932800-85946600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:85933000-85940200	Weak transcription	Esophagus	oesophagus
8	chr2:85933600-85937000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:85933600-85938200	Weak transcription	Gastric	stomach
10	chr2:85933600-85938600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr2:85934200-85937000	Weak transcription	Spleen	Spleen
12	chr2:85934200-85941400	Enhancers	Brain Anterior Caudate	brain
13	chr2:85934400-85937000	Weak transcription	Fetal Thymus	thymus
14	chr2:85934400-85937000	Weak transcription	Left Ventricle	heart
15	chr2:85934400-85937000	Weak transcription	Lung	lung
16	chr2:85934400-85937000	Weak transcription	Psoas Muscle	Psoas
17	chr2:85934400-85937000	Weak transcription	Right Ventricle	heart
18	chr2:85934400-85940000	Weak transcription	Pancreas	Pancrea
19	chr2:85934600-85937000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:85934800-85937000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:85934800-85937000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:85934800-85937400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:85934800-85938000	Weak transcription	HSMMtube	muscle
24	chr2:85934800-85938200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:85934800-85940400	Weak transcription	HMEC	breast
26	chr2:85935000-85937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:85935000-85937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:85935200-85937200	Weak transcription	Stomach Mucosa	stomach
29	chr2:85935600-85937200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:85935600-85939000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:85935600-85939400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:85935800-85937000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:85935800-85938800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:85935800-85939000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:85935800-85939400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:85935800-85941200	Enhancers	Brain Substantia Nigra	brain
37	chr2:85935800-85941400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:85935800-85941400	Enhancers	Ovary	ovary
39	chr2:85936000-85940600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:85936200-85937000	Enhancers	Rectal Smooth Muscle	rectum
41	chr2:85936200-85940200	Enhancers	Primary B cells from cord blood	blood
42	chr2:85936400-85937200	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:85936400-85937200	Enhancers	NHLF	lung
44	chr2:85936400-85937400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr2:85936400-85940600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr2:85936400-85941600	Enhancers	Right Atrium	heart
47	chr2:85936600-85937200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:85936600-85937200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:85936600-85937200	Bivalent Enhancer	Osteobl	bone
50	chr2:85936600-85937600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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